Points of View: Neural circuit diagrams

Journal name:
Nature Methods
Volume:
13,
Page:
189
Year published:
DOI:
doi:10.1038/nmeth.3777
Published online

Use alignment and consistency to untangle complex circuit diagrams.

At a glance

Figures

  1. Use color and shape consistently to encode the type of connection and cell.
    Figure 1: Use color and shape consistently to encode the type of connection and cell.

    (a) Use line caps or colors, but not both, for excitory (exc), inhibitory (inh) and neuromodulatory (mod) connections. Use colorblind-safe colors3. (b) A busy circuit diagram challenged by tight spacing and angled elements. Figure adapted with permission from ref. 4. (c) Applying consistent size, spacing and alignment of elements without rotation allows for the inclusion of additional relevant information, such as two populations of BNST neurons.

  2. Simplifying node arrangement and discarding unnecessary variables creates clear circuit diagrams without loss of information.
    Figure 2: Simplifying node arrangement and discarding unnecessary variables creates clear circuit diagrams without loss of information.

    (a) Placing nodes in a neural circuit anatomically makes routing edges difficult and patterns hard to spot. Adapted from ref. 5 with permission from Elsevier. (b) Same circuit with fewer edge crossings and without redundant color. (c) Same circuit with emphasis on node A. Curved edges assist eye movement.

  3. Maintenance of brain region topology is necessary for some circuit diagrams.
    Figure 3: Maintenance of brain region topology is necessary for some circuit diagrams.

    (a) Hypothetical cortical microcircuit depicted with common diagram errors: too much morphological detail, inaccurate or ambiguous edge paths, unnecessary variables and weak neurotransmitter encoding. (b) Clarified circuit diagram with emphasis on the two different output regions.

  4. Strategies to add emphasis and information to the circuit shown in Figure 1.
    Supplementary Fig. 1: Strategies to add emphasis and information to the circuit shown in Figure 1.

    Full region acronyms are shown as in the original5.

References

  1. Hunnicutt, B.J. & Krzywinski, M. Nat. Methods 13, 5 (2016).
  2. Wong, B. Nat. Methods 8, 611 (2011).
  3. Wong, B. Nat. Methods 8, 441 (2011).
  4. Cook, J.B. J. Neurosci. 34, 58245834 (2014).
  5. Zingg, B. et al. Cell 156, 10961111 (2014).

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Author information

Affiliations

  1. Barbara Jeanine Hunnicutt is a freelance data scientist.

  2. Martin Krzywinski is a staff scientist at Canada's Michael Smith Genome Sciences Centre.

Competing financial interests

The authors declare no competing financial interests.

Author details

Supplementary information

Supplementary Figures

  1. Supplementary Figure 1: Strategies to add emphasis and information to the circuit shown in Figure 1. (483 KB)

    Full region acronyms are shown as in the original5.

PDF files

  1. Supplementary Figure (603 KB)

    Supplementary Figure 1

Additional data